Choices
by KiyoshiMichi
Summary: Shepard had life-altering decisions to make and all the consequences to include.   ME3 compliant, Kaidan/Shepard romance option


Oke, I have played ME3 four times all the way through in less than 2 weeks. I hated the endings... even though I got a perfect... plus, I watched the Kaidan/Shepard scene 6+ times and came to the conclusion - KAIDAN IS A POWERTOP! I didn't really portray that in here, but that's just what I think... even though I would NOT have put that with his personality and Shepard's own.

Anyway, I wanted to end on a slightly funny note, but also emphasizing how Shepard changed in seven years (you all will see) so... I dunno... I also wrote 90% of this at my friend's house today while staring at an artist rendition of a turian/human hybrid (which was hot by the way) and nerding over ME.

Warnings: Um... homosexuality based off the Kaidan/Shepard romance option. Plus... depression and other stuff...

Disclaimer: BioWare owns ME but I OWN NEEKEV! And the system and planet... those are mine... back off.

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><p>Choices<p>

ME AU

By:

Kiyoshi Michi

He stared hard at the three glowing areas in front of him, still holding his bleeding torso. He hurt. He hurt all over in a way he had never had to deal with before, even right before his death. But this choice was important, oh so very important.

After all, Shepard was once again making a choice that would either save all life in the galaxy or only fuck it up further.

He already knew that synergy was out of the question. For everything that had happened – all the people that had been lost, all the planets close to decimated – it just did not seem to be a very satisfying ending. The Reapers got away with everything by having a peaceful 'ending.'

It hardly seemed to be fair to everyone else in the Milky Way who had already suffered.

Now though, he had to choose between controlling the Reapers and destroying them. It should have been cut and dry, but since either option was apparently going to kill him and many others regardless, he was conflicted.

On the one hand, he could control the Reapers and force them away. Shepard could demand – persuade – the behemoths to leave all the planets they had taken. However, that would mean leaving them alive and how was he to know with one hundred percent certainty that he would not go insane like the Illusive Man did.

On the other hand, he could destroy the Reapers. He could get the revenge that everyone wanted in this final battle. But that would mean destroying the Mass Relays, the Geth, and even himself for he was partly synthetic now.

Going over that once again, he realized he had known the answer all along.

With newfound determination, Shepard began to limp away from that weird ass star child and toward the pillar glowing red. He was going to destroy those damned Reapers once and for all.

It took so much longer than Shepard would have liked, and he spent the time thinking about everyone he knew, everyone who had been sacrificed for the galaxy, not just this battle.

Mordin had gone out like a true hero, saving the very people his own worked to destroy.

Ashley had left them early on and Shepard had never forgotten how she left them.

Legion, unfortunately, had to be shot in the end but he died with a soul – Tali had told him so before he ceased to exist.

Miranda had died protecting her sister and to give Shepard the information he would need to get the Catalyst back from Kai Leng.

His mind moved to the ones who lived. Liara, the wonderful asari who was like the sister he never had. Garrus, his brother in arms and the best friend he could have gotten in this hectic life. Grunt, the amazing krogan he would easily trust his life to in the worse of situations. Jack, the tough woman who whipped Shepard back to the man he was after every incident that made him question himself. Tali, the little tech geek who made sure to bring some levelheaded ideas to most situations. Joker, the best pilot in the galaxy and one of few men who could get the Commander to laugh. EDI, an AI that made Shepard realize how human he was in her quest for humanity.

As he neared the glowing red pod and lifted the gun, he thought of one final person – Kaidan Alenko.

He still remembered that shy lieutenant that followed him around, constantly suffering from horrible headaches. He very much remembered the incident on Horizon that left him a little broken and empty inside, though he had been unsure why. Shepard even thought back to when he met Kaidan again, and how they had been forced back together, separated once again, then Kaidan volunteered to come back.

Shepard had been so happy that the Major had offered to return to the Normandy. It felt so foreign without Kaidan. He finally realized why during the conversation with Kaidan when said man was in Huerta. Though Shepard did not quite remember how it got to that point, he still remembered when Kaidan asked if he was flirting with him, then told him not to answer so he could live in the illusion.

That had gotten the Commander thinking afterwards. He even spoke to Liara about it, which had caused the asari to chuckle. Apparently, she thought it was 'cute' and told him that if he wanted an intimate relationship as well, he should definitely go for it when Kaidan got out.

Shepard had done just that, though it took a little longer than he thought with all the missions and Kaidan was the one who actually suggested a relationship to him. As soon as the option came up, Shepard was quick to agree. That had, apparently, surprised the Major since he looked so shocked that not only would Shepard not be disgusted, but agreed to easily.

That was the start of their relationship and right before this final battle, they did make love (since Shepard felt an odd lack of emotion in the phrase 'had sex').

That was his last thought as he began shooting at the pod until it exploded and everything went black as he was knocked out.

* * *

><p>"Doctor, it…. It's been a month. Has he… gotten better?"<p>

"I'm sorry, Major Alenko, but there has still been no progress in the Commander's condition."

His head was pounding, he wanted them to shut up. He could feel his facial muscles pulling into a sneer as he cracked open his red eyes, just enough to make out two figures at the end of his bed. Why the hell were two people in his room?

"Would you both… shut up…?"

There was sudden silence that relaxed Shepard as he moved back into a comfortable position. He rested there for a few seconds before something hit him – he was alive. He suddenly bolted upright, which caused more pain than he would have liked, and stared down at his own body. It was battered and bruised, but definitely still useable and very much alive.

The Commander then finally looked around and realized he was in a hospital room, much like the one Kaidan had been in.

"Shepard…?"

He recognized that voice, he knew he did. He barely had time to realize it was Kaidan before arms suddenly wrapped tightly around his neck and shoulders. It was a strange thing to notice before returning the hold, but Kaidan's arms, and entire body really, were shaking noticeably.

He could even feel the wetness that accompanied tears falling onto his shoulder.

Well, that was starting to make Shepard feel guilty. He really had not thought about what would happen if he lived. He had prepared himself to die to save the galaxy so he did not think he would have to deal with people who had mourned him again.

"Hey Kaidan… it's all right..."

"Shepard, we… we couldn't find you at first. I… I was certain you were dead since it took us two months to even find you. Even then, after two months, you were so banged up and no one was sure how you made it. Two months…. Two months without any medical care, water, or food. Anyone else would have died from dehydration or malnutrition long before we found them.

"In fact… they would have been hard to identify by time we got to them. The doctors can't make sense of it… I can't make sense of it. It's almost like… you were in some form of stasis until we found you…"

Shepard had noticed that as Kaidan continued to talk, his voice sounded more and more strained. It started to crack with every other word and he continuously had to take deep breaths. Somehow, he knew what he had to do.

"Kaidan… everything is all right now. The Reapers are gone, the galaxy is safe, and we are all still alive. I'm alive."

It took a few moments, but Kaidan's shoulders finally sagged and he pulled his arms from around the Commander's shoulders. He heaved a sigh and flopped back into the chair pulled up next to the bed. Shepard watched him run his hands over his face, through his hair, and back to his face where they rested.

Shepard was still feeling guilty, especially when Kaidan started speaking again. "You know… I forced them to keep searching, long after a second funeral was held for you." Kaidan chuckled, though it was forced and strained. "Commander Shepard, the only man to have three funerals… at least."

He wanted to say he was not going to 'die' again, but Kaidan kept going. "But… I didn't go to your second funeral. Once was… enough. A second time would have broken me completely. Besides, if I had gone, it would have meant… I was giving up. I couldn't do that. Not when you came back after two years the last time. I thought 'well, anything could happen.' Apparently… anything can happen."

The Commander listened to Kaidan heave another sigh, digging his palms into his eyes. The poor man seemed so worried, so Shepard began to wonder if he should tell Kaidan what he had decided long ago regarding what he would do if he happened to live. It might put him at ease just a little… and put Shepard's guilt at ease.

"I don't think you will have to worry too much about me dying anymore."

Kaidan peered through his fingers, looking understandably skeptical. After all, Commander Shepard was known throughout the Milky Way as being someone who could turn a routine mining mission or Alliance base check into a deadly fire fight mixed with exploding buildings and near death experiences just walking.

"I think… I'm going to retire. Or at the very least, demand something like a desk job."

Kaidan blinked a few times and pulled his hands from his face, looking very confused. Shepard could understand though. In anyone else's shoes, they could probably only think 'the great Commander Shepard getting a desk job? That's not right – he belongs on the battlefield.'

"… desk job?"

Yeah, that was exactly what Kaidan was thinking.

"Yeah. I'm not old by a long shot, but I have already done more than any other fleet in any system could hope to accomplish. I took out Saren and Sovereign, went through the Omega 4 relay and destroyed the Collector base – a suicide mission where everyone lived by the way, I took down the Illusive Man and Cerberus, I destroyed all the Reapers in a single moment. Let's not forget that I came back from the dead once and cheated it the second time.

"I think I have done enough on the 'battlefield' to last the rest of my natural life. Don't you agree?"

Kaidan nodded dumbly, staring at Shepard like he had grown a second head… maybe even a third with six eyes a piece and sprouted tentacles. "You… really want a desk job?"

"Well, I know that doing nothing all day would drive me insane, so I need something. However, I just think I'm done with the high-risk, adrenaline-fueled missions. Even now, I can tell my leg is still fucked up."

"The… uh… doctor said you would have a limp for the rest of your life."

"And that is just another reason to not be out doing something so dangerous."

Shepard could tell that Kaidan was seriously thinking all this over. Finally, the Major just nodded and leaned back in the chair. Shepard knew Kaidan still had a little further to go before he could say he was past this whole thing as much as he could be.

"Now then… since I did not get the chance to bust you out of here before, think you can help me escape?"

Kaidan smiled and shook his head. "Sorry, Shepard. You weren't in time before so I owe you nothing in regards to the hospital."

"Can you at least make sure I get some good food every now and then?"

"Now that I can do."

* * *

><p>Shepard had been true to his word. After months of slipping in and out of small comas and serious physical therapy, the Commander had gotten a desk job in a very nice office with a soothing view. Well… it was mostly a desk job… similar to what Commander Bailey did in C-Sec.<p>

Which was exactly where Shepard was.

Sometime during the months he was incapacitated, they had found a way to rebuild the Citadel at speed the Commander had not thought possible.

So, they had needed more personnel, and he was quite happy to give up his frontline, battlefield position to sit at a desk or chase petty criminals across Presidium Commons. He even dealt with the drunks down at Purgatory, now run by someone Aria trusted as much as she could trust someone.

Shepard found himself content, though sometimes bored out of his mind. Currently, he was in one of those bored slumps since Kaidan had been gone for almost two weeks. Shepard understood that Kaidan would sometimes be gone for long periods of time, since he had chosen to stay with the Normandy crew. The Major had said he still had the heart to continue with the dangerous missions, though they were never quite as dangerous as the ones Shepard had led his crew into.

Still, he typically at least sent a message or something. So far, Shepard had gotten nothing and not only was he lonely, he was getting very concerned. He sighed and dropped his head into his hands, fingers massaging his forehead. This was the scene Commander Bailey found when he walked into the office.

"Shepard, something wrong?"

"Ugh…" The man peered through his fingers, brows furrowed. "I'll tell you but… you can't tell people that the great Commander Victor Shepard has real emotions and feelings, all right?"

Since it had been a long running joke between the two, Bailey just laughed and nodded, taking a seat in one of the chairs near the desk. "All right. Anything to save the reputation of Shepard."

"Good. Now, you damn well know about me and Kaidan since… that incident." Bailey made a face – he remembered that all too well. The two together did not bother him, but the scene sure had. "You also know that while I took this desk job, he decided to stay on board the Normandy. Well, he's been gone two weeks and though two weeks is a normal amount of time, short even, he has not contacted me once. So, I am getting worried."

Bailey leaned back in the seat and rubbed his chin in thought. Normally, he would have suggested that the other party might be cheating since there had been no reports of crashes or the like recently. However, Kaidan followed Shepard around like a lost puppy during the times he was on the Citadel.

Bailey highly doubted Kaidan would stray like that. It just did not fit the Major.

But, he did not want to say that maybe something had happened. Bailey knew the entire mission report and what Kaidan and the Normandy had gone to do, but Shepard did not. He was not sure he should tell the Commander the truth… but if he didn't… Bailey sighed and rested his cheek on his knuckles.

"To be honest, I think there really isn't that much to worry about right now. Maybe, communications have gone offline or something."

Shepard nodded. "Yeah… you're right. I should hear from him soon."

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><p>Four months later, and Bailey could see that Shepard was slowly becoming a wreck. The man would stare vacantly at the wall, his face unreadable but his red eyes full of so many emotions – hope, despair, love, regret. Really, it was tearing everyone apart inside the moment those eyes turned their way.<p>

Eight months after Kaidan's disappearance, and Shepard's hair, which had been bleached white, was now naturally white. His dark tan skin was getting paler as the days went by. Even his eyes were starting to change. They were becoming filled with more and more hopelessness.

A year and a half after Kaidan's disappearance, Shepard was starting to seem like a robot. His eyes were glazed all the time. He threw himself into work and exercise, never sleeping. Bailey knew of the nightmares – he had to wake Shepard from one when he fell asleep at his desk.

Three years after Kaidan's disappearance, Bailey had to make sure Shepard took care of necessities during the day. If Bailey forgot to say anything, Shepard would forget to shower or eat, though he at least still got up to use the restroom every so often.

Five years after Kaidan's disappearance, Shepard changed again. No one would say he had gotten over Kaidan but rather, he was done doing nothing. Now, he did nothing but work and work hard. He was making more arrests than ever before. But his eyes… people would whisper about how soulless his eyes were.

Seven years after Kaidan's disappearance, people could tell Shepard was nearing his limit. They began to worry he would take his own life. Even Bailey was concerned and about to go visit the man like he did every day, but a call stopped him.

"Hello, this is Commander Bai- what?"

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><p>Shepard was in his office, his cheek resting against the cool desk. He had not seen Bailey in two days, which was really weird. The man made it a point to check up on him every day. Shepard felt like he probably would have taken his own life years ago if Bailey had not tried so hard to keep him from doing so.<p>

As it was, he was seriously contemplating the idea now. He wanted so badly to believe that Kaidan was alive, but it had been seven years since he had gone missing. Bailey had to try so hard to keep the Council from changing his status from MIA to KIA.

Shepard was losing faith as well… in fact, he felt like he had run out of it. He could be so patient but… he was so tired of waiting with nothing happening.

"Holy shit! Victor!"

Shepard's head snapped up so quickly, he swore he would get whiplash. But, why the hell would he care? A fucking ghost was standing in his doorway, face full of concern. Wait… ghosts did not look quite so solid.

"… Kaidan?"

"Damn, what the hell happened to you!" Shepard was reeling from seeing the face of his lover, whom he was starting to believe was dead. "You look horrible… you're paler than I am now."

Shepard reached out and ran his fingers over Kaidan's face, stopping his next comment before it really started. He had to know if Kaidan was solid, had to know if he was really there. So far, his fingers were resting solidly on his face. He even poked and prodded some, completely silent from the amazement he felt.

Finally, Kaidan just sighed and pushed the hands away, smiling like everything was all right. "I didn't know the great Commander Shepard was so melodramatic. It's only been a few weeks."

Shepard stared at Kaidan. How the hell could he say that? Did Kaidan not know how much time had passed, how Shepard had given up hope, mourned, and was so close to taking his own life? Shepard couldn't look at Kaidan right then – he had to tell the man, but first, he needed to know what happened.

"Kaidan… what happened? During your mission…"

"Ah, yes. Now, this is actually quite the interesting story. So, when we left three weeks ago-" Shepard had to keep himself from choking. "We were headed for a system I had never heard of before. Somewhere called the Daskeen Kelur system, where there was only a sun in the last stage of life and a tiny planet called Xeraxiss.

"I know you wouldn't like this, but we were called out with a few other fleets because there were reports from the ruler of the people there, saying somehow, someway, a rogue Reaper had survived the blast that killed the rest. Luckily, it was one of the… uh… 'small' ones. But this ruler, Neekev, did not have enough military strength because of civil strife from the previous ruling.

"Thus, we were sent out. Oddly enough, this Reaper was harder to destroy than we thought. Then again, it did survive that moment when all other Reapers lived. Now, it took a few days, but we did manage to get just enough firepower to take the Reaper down. But, right before we did, it sent out this wave that knocked the entire crew out for a few hours. When we came to, Alliance troops were on the Normandy, waking everyone and making sure we got back to the Citadel."

Saying Shepard was shocked was an understatement.

"So… you were all put into stasis…?"

"What? No, we were just knocked out for a few hours."

Shepard shook his head and let it fall into his hands. He was feeling this odd mixture of relief, guilt, and sorrow. "Kaidan… look at me. A man does not change like I did in three weeks. You don't… you don't know… how close I was to giving up on my own life. You don't know how often I would wake, turn over to kiss you or pull you close, and you weren't there. You don't know how long I waited for contact but was left in the dark.

"Kaidan… you've been gone… for seven years."

Shepard could practically feel himself drowning in the silence that followed, not ready to look up. Kaidan had not even known that seven years of his life was gone until Shepard had told him. He didn't know that Shepard had suffered and agonized for seven long years.

It wasn't the first time since Kaidan's disappearance that the Commander wished he was still on the Normandy, but it was the one time he felt such a drive to hunt down something already dead, bring it back, torture it, and kill it again.

He startled some when he felt a weight on his back and arms wrap around him from behind. Seven years ago, he had been used to this sort of contact. It moved to craving it then getting annoyed with anyone who touched him, then becoming unaccustomed.

"Wha… Kaidan?"

"You know… I may have lost seven years of my life because I was in stasis and I will need time to get used to that. But you… you were awake – aware – for that entire time." Shepard had learned what Kaidan had felt when Shepard had gone missing, but even Kaidan would agree that Shepard's ordeal was so much worse. "I know you'll also need time to get used to everything again… but I'm here now. We're both alive and we're together."

Shepard stared at the arms around his chest before awkwardly reaching up to latch onto Kaidan's forearm. He absolutely still loved Kaidan – he wouldn't even look at another person the entire seven years Kaidan was missing. But Shepard was so unused to physical contact like this and it took awhile the first time to officially be 'used' to it.

"Yeah… you're right."

"Of course I am." Shepard could feel one corner of his lips quirking upwards, but it died quickly. Give him enough time and he would laugh with Kaidan like he did before. "Now then, we're going to leave this office, go back to the apartment – which I am praying we still have, and I am going to force to relax for at least a week while spending the same amount of time getting you used to cuddling again."

Shepard didn't even make a sound of protest as Kaidan grabbed his arm and tugged him from the chair, careful to give him enough time to stabilize himself. When the Commander was balanced, the Major dragged him from the room and over to the elevator, passing Bailey on the way.

"Commander Bailey, I am kidnapping Commander Shepard from you for an indefinite amount of time. You know… nurse him back to health, become his psychiatrist until he's normal Shepard, and… you know… stuff like the infamous incident."

Bailey was all right, until the 'incident' was brought up. "That's fine by me… but can we please stop telling me about your relationship in regards to… the incident?"

Kaidan snorted and shook his head, causing Bailey to nearly faint when he saw the quirk in Shepard's lips, like a smile. Finally, the pair disappeared into the elevator and Bailey was left shaking his head. Garrus, who had actually retired around the time Shepard chose a different job and moved to the Presidium as well, walked up to Bailey and chuckled.

"Well, it's nice to see that Shepard is not completely beyond all hope. But… there is one thing I am very curious about."

"What?"

"What exactly is this… incident you all keep talking about?"

"… I walked into the office to greet Shepard on his first day… and found them fucking over the desk."

"… I am so sorry I asked."

_End._

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><p>And... there you have it. I like it... but meh, tell me what you think.<p> 


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